Detection of DNA Using a Visible Dye, Nile Blue, in Electrophoresed Gels

Yang, Yong-Il; Hong, Hoang Thi Kim; Lee, Ik‐Soo; Bai, Dong-Gyu; Yoo, Gyurng-Soo; Choi, Jung-Kap

doi:10.1006/abio.2000.4537

Cited by 42 publications

(17 citation statements)

References 6 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…It became obvious from the experiments that different forces are responsible for encapsulating the dye prior to and after polymerization. We hypothesize that, if the dye is added after polymerization, similar to staining DNA (Yang et al 2000;Chen et al 1999) and other proteins and macromolecules such as RNA and BSA (Lee et al 2003), hydrogen bonding, hydrophobic interactions, and Van der Waals forces are responsible for keeping it in the PEG. In addition, the positively charged amino group of the dye could be attracted to the partial negative charge of the ketone group in the polymer.…”

Section: Resultsmentioning

confidence: 99%

“…With NB being a solvatochromic dye, a blue shift of both peaks is noted with increase of ethanol concentration. This is a typical behavior for most dyes (Yang et al 2000), and thus a fluorescence intensity ratio (688 nm/700 nm) Â (625 nm/640 nm) accounting for the degree of the shift was adopted in building the calibration curve. A calibration function in the concentration range of 0 -90% v/v was established.…”

Section: Calibration Sensitivity and Response Timementioning

confidence: 99%

See 1 more Smart Citation

Optical Ratiometric Sensor for Alcohol Measurements

et al. 2007

View full text Add to dashboard Cite

The need for low-cost, robust alcohol sensors has increased with the renewed interest in alternative fuels as well as high-throughput screening of biological processes involving the production of ethanol. The goal of this research was to develop a miniaturized optical ratiometric ethanol sensor to be used for in situ measurements. The sensor is based on the fluorescent dye Nile Blue Chloride. When in solution, the dye exhibits a single fluorescence peak. However, a dual emission peak is observed upon physical immobilization of the dye in the hydrogel poly(ethylene glycol) dimethacrylate. The dual emission allows for ratiometric measurements, thus circumventing drawbacks associated with fluorescence intensity measurements such as signal variations due to dye bleaching, source intensity fluctuations, etc. In developing this sensor we investigated ethanol sensitivity; alcohol selectivity; response time; and cross-sensitivity with pH, polarity, and ionic strength. We found that the sensor is sensitive to a broad range of ethanol concentrations, namely 5% to 90% v/v. Due to the hydrogel's restrictive pore size, the sensor is sensitive to short-chain alcohols such as methanol, ethanol, and propanol, but lacks sensitivity to larger alcohols such as butanol and hexanol. We also found the sensor maintains full functionality after autoclaving. Sensor sensitivity to alcohol in solutions of varying ionic strength is negligible, whereas the solvent's polarity must be controlled to maintain meaningful results. The sensor is most sensitive in acidic and neutral environments, indicating promising use for yeast-based alcohol fermentations.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Calibration Sensitivity and Response Timementioning

confidence: 99%

Optical Ratiometric Sensor for Alcohol Measurements

et al. 2007

View full text Add to dashboard Cite

show abstract

“…Several protocols for detecting DNA in agarose or polyacrylamide gels using visible dyes, such as methylene blue, [6,7] brilliant cresyl blue, [8] crystal violet, [9,10] and ethyl violet, [11] have been described previously. [12,13] These methods are simple and safe but require long staining times and provide low sensitivities.…”

Section: Introductionmentioning

confidence: 99%

A New Organic Dye-Based Staining for The Detection of Plant DNA in Agarose Gels

Sönmezoğlu

Özkay

2015

Nucleosides, Nucleotides and Nucleic Acids

View full text Add to dashboard Cite

Ethidium bromide (EtBr) is used to stain DNA in agarose gel electrophoresis, but this dye is mutagenic and carcinogenic. We investigated N-719, which is a visible, reliable and organic Ruthenium-based dye, and five fluorescent alternatives for staining plant DNA. For prestaining and poststaining, N-719, GelRed, and SYBR Safe stained both DNA and PCR product bands as clearly as EtBr. SYBR Green I, methylene blue, and crystal violet were effective for poststaining only. The organic dye N-719 stained DNA bands as sensitively and as clearly as EtBr. Consequently, organic dyes can be used as alternatives to EtBr in plant biotechnology studies.

show abstract

“…It has been used as a red-region nucleic probe in histological staining of biological preparations [4], DNA electrophoresis [5], photodynamic therapy of malignant tumours [6], fluorescent label in DNA biosensors [7], and spectrophotometric studies of NB interaction with nucleic acids [8][9][10]. The planar hydrophobic phenoxazine moiety of NB is expected to facilitate the intercalation of NB into the relatively non-planar interior of the DNA helix.…”

Section: Introductionmentioning

confidence: 99%

Investigation of specific interactions between Nile blue and single type oligonucleotides and its application in electrochemical detection of hepatitis C 3a virus

Alipour

Allaf

Mahmoudi-Badiki

2015

J Solid State Electrochem

View full text Add to dashboard Cite

In this study, development of an electrochemical DNA biosensor based on a hepatitis C virus probe was introduced using an electrochemically pre-treated pencil graphite electrode (PPGE) as a transducer and Nile blue (NB) as an electroactive indicator. At first, the electrochemical behaviour of NB on the PPGE was investigated. Then, elucidating the specific interaction of NB with each of the nucleotides of DNA, the interactions of NB with oligonucleotides containing only one base type were studied. In this study, four 18-mer oligonucleotides of poly A, poly T, poly C, and poly G were used as probe and were used as related complementary/noncomplementary sequences in the hybridization section. The extent of hybridization was evaluated based on the difference between DPV signals of NB accumulated on the probe-PPGE and NB accumulated on the probe-target-PPGE. Then, the developed biosensor was applied successively for the detection of short sequences of Hepatitis C 3a virus (14 pic). The hybridization between the probe (14 pic) and its complementary sequence (C 2 Comp) as the target was studied. Some hybridization experiments with noncomplementary oligonucleotides also showed that the suggested DNA sensor responds selectively to the target. Diagnostic performance of the developed biosensor was described and the detection limit was found to be 1.1 nM with a relative standard deviation of 3.5 % in the 0.1-M Tris-HCl buffer solution (pH 7.0) containing 20 mM NaCl.

show abstract

Detection of DNA Using a Visible Dye, Nile Blue, in Electrophoresed Gels

Cited by 42 publications

References 6 publications

Optical Ratiometric Sensor for Alcohol Measurements

Optical Ratiometric Sensor for Alcohol Measurements

A New Organic Dye-Based Staining for The Detection of Plant DNA in Agarose Gels

Investigation of specific interactions between Nile blue and single type oligonucleotides and its application in electrochemical detection of hepatitis C 3a virus

Contact Info

Product

Resources

About